Using phylogenetic information and the comparative method to evaluate hypotheses in macroecology
Article first published online: 19 FEB 2013
© 2013 The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society
Methods in Ecology and Evolution
Volume 4, Issue 5, pages 401–415, May 2013
How to Cite
Hernández, C. E., Rodríguez-Serrano, E., Avaria-Llautureo, J., Inostroza-Michael, O., Morales-Pallero, B., Boric-Bargetto, D., Canales-Aguirre, C. B., Marquet, P. A., Meade, A. (2013), Using phylogenetic information and the comparative method to evaluate hypotheses in macroecology. Methods in Ecology and Evolution, 4: 401–415. doi: 10.1111/2041-210X.12033
- Issue published online: 16 MAY 2013
- Article first published online: 19 FEB 2013
- Manuscript Accepted: 6 DEC 2012
- Manuscript Received: 30 DEC 2011
- FONDECYT. Grant Number: 11080110
- Bayesian inference;
- character evolution;
- directional comparative method;
- diversification rate;
- PGLS ;
- It is widely recognized that macroecological patterns are not independent of the evolution of the lineages involved in generating these patterns. While many researchers have begun to evaluate the effect of ancestor–descendant relationships on observed patterns using the phylogenetic comparative method, most macroecological studies only utilize the cross-sectional comparative method to ‘remove the phylogenetic history’, without considering the option of evaluating its effect without removing it.
- Currently, most researchers use this method without explicitly evaluating three fundamental evolutionary assumptions of the comparative method: (i) that the phylogeny is constructed without error (which implies evaluating phylogenetic uncertainty); (ii) that more closely related species tend to show more similar characters than expected by chance (which implies evaluating the phylogenetic signal) and; (iii) that the model of the characters' evolution effectively recapitulates their history (which implies comparing the fit of several evolutionary models and evaluating the uncertainty of the estimating model parameters).
- Macroecological studies will benefit from the use of the comparative method to assess the effect of phylogenetic history without removing its effect. The comparative method will also allow for the simultaneous analysis of trait evolution and its impact on diversification rates; it is important to evaluate these processes together because they are not independent. In addition, explicit evaluations of the assumptions of comparative methods using Bayesian inferences will allow researchers to quantify the uncertainty of specific evolutionary hypotheses accounting for observed macroecological patterns.
- We illustrate the usefulness of the method using the phylogeny of the genus Sebastes (Pisces: Scorpaeniformes), together with data on the body size–latitudinal range relationship to estimate the effect of phylogenetic history on the observed macroecological pattern.